Introduction: Hospital-acquired Malnutrition occurs as a result of reduction in food intake, increased dietary loss and/or increased calorie requirements as a result of disease-induced high catabolic state. A child's nutritional status often deteriorates after admission to the hospital resulting in longer duration of hospital stay and increased risk of complications, which also increases treatment cost. Hospital-acquired Malnutrition is usually assessed using anthropometric measurements and/or serum pre-albumin. Objectives: This study sought to investigate the incidence of Hospital-acquired Malnutrition using anthropometric measurements and to determine diagnostic utility of serum pre-albumin in predicting weight change. A secondary objective was to identify factors associated with Hospital-acquired Malnutrition in children admitted at Aga Khan University Hospital, Nairobi. Methodology: This was a hospital-based, short follow up longitudinal survey carried out on children admitted to Aga Khan University Hospital, Nairobi. One hundred and eighty children were enrolled into the study. Weight and height were taken at admission and discharge. Serum pre-albumin levels were taken at admission and repeated after 48-96 hrs. Data Analysis: The incidence of Hospital-acquired Malnutrition was estimated from the total number of children showing a decrease in weight-for-height/length or BMI Z-scores from the time of admission to discharge. Sensitivity, specificity, positive and negative predictive values of serum pre-albumin were calculated to determine its diagnostic utility in screening for Hospital-acquired Malnutrition. Levels of serum pre-albumin were summarized using a Pre-albumin Risk Stratification model by Bernstein et al. Logistic Regression Analysis, with calculation of odds ratio, was done for selected variables to look for any association with loss of weight during hospitalization. Results: The study showed that 103 (60.6%) children lost weight from admission to discharge, giving a mean weight decrease of 0.5kg (SD±3.37), p=0.055. Of the 170 children studied, 109 who were ≤60 months of age, demonstrated a mean decrease in weight-for-height/length Z-score of 0.145 (SD±0.73), p=0.042, and 61 children aged >60 months demonstrated a mean decrease in BMI Z-score of 0.152 (SD±0.39), p=0.004. Nine percent (10/109) of children ≤60 months and 3.0% (2/61) of children >60 months had worsening of nutritional status as determined by WHO classification. The greatest frequency of weight loss was observed among children diagnosed with gastroenteritis (81.2%), gastritis (64.3%) and pneumonia (55.6%). LOS was demonstrated to be the most significant risk factor for weight loss (OR 1.37, p=0.003, C.I 1.11-1.69). Children who had a hospital stay of 5-7 days had about 4.5 fold risk for weight loss (OR 4.67, 95%